Merge remote-tracking branch 'upstream/main' into jabrefonline

* upstream/main: New Crowdin updates (#7843) Refactoring and addition of unit tests (#7597) CLI option to write XMP metadata to pdfs (#7814) Add query validation for web search (#7809) change eclipse default output dir (#7842) Bump lucene-queryparser from 8.8.2 to 8.9.0 (#7835) Bump libreoffice from 7.1.3 to 7.1.4 (#7836) Bump postgresql from 42.2.21 to 42.2.22 (#7839) Bump org.eclipse.jgit (#7838) Bump byte-buddy-parent from 1.11.2 to 1.11.5 (#7837) Bump unoloader from 7.1.3 to 7.1.4 (#7841) Ms Office Export patent author as inventor (#7831) Abbreviation toggle within the JournalEditorViewModel now ignores curly braces (issue #7773) (#7807)
JabRef · Jun 22, 2021 · bd5ab5b · bd5ab5b
2 parents b79bf7e + b6697fe
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -28,9 +28,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added a select all button for the library import function. [#7786](https://github.com/JabRef/jabref/issues/7786)
 - We added a search feature for journal abbreviations. [#7804](https://github.com/JabRef/jabref/pull/7804)
 - We added auto-key-generation progress to the background task list. [#7267](https://github.com/JabRef/jabref/issues/72)
+- We added the option to write XMP metadata to pdfs from the CLI. [7814](https://github.com/JabRef/jabref/pull/7814)
 
 ### Changed
 
+- The export to MS Office XML now exports the author field as `Inventor` if the bibtex entry type is `patent` [#7830](https://github.com/JabRef/jabref/issues/7830)
 - We changed the EndNote importer to import the field `label` to the corresponding bibtex field `endnote-label` [forum#2734](https://discourse.jabref.org/t/importing-endnote-label-field-to-jabref-from-xml-file/2734)
 - The keywords added via "Manage content selectors" are now displayed in alphabetical order. [#3791](https://github.com/JabRef/jabref/issues/3791)
 - We improved the "Find unlinked files" dialog to show import results for each file. [#7209](https://github.com/JabRef/jabref/pull/7209)
@@ -49,6 +51,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - The tooltip of the search field explaining the search is always shown. [#7279](https://github.com/JabRef/jabref/pull/7279)
 - We rewrote the ACM fetcher to adapt to the new interface. [#5804](https://github.com/JabRef/jabref/issues/5804)
 - We moved the select/collapse buttons in the unlinked files dialog into a context menu. [#7383](https://github.com/JabRef/jabref/issues/7383)
+- We fixed an issue where journal abbreviations containing curly braces were not recognized  [#7773](https://github.com/JabRef/jabref/issues/7773)
 
 ### Fixed
 

diff --git a/build.gradle b/build.gradle
@@ -133,8 +133,8 @@ dependencies {
 
     implementation 'commons-cli:commons-cli:1.4'
 
-    implementation 'org.libreoffice:libreoffice:7.1.3'
-    implementation 'org.libreoffice:unoloader:7.1.3'
+    implementation 'org.libreoffice:libreoffice:7.1.4'
+    implementation 'org.libreoffice:unoloader:7.1.4'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.10'
     implementation 'info.debatty:java-string-similarity:2.0.0'
@@ -145,18 +145,18 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.9.2'
     implementation 'org.antlr:antlr4-runtime:4.9.2'
 
-    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.8.2') {
+    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.9.0') {
         exclude group: 'org.apache.lucene', module: 'lucene-sandbox'
     }
 
-    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.11.1.202105131744-r'
+    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.12.0.202106070339-r'
 
     implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.12.3'
     implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.12.3'
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.3'
 
-    implementation 'org.postgresql:postgresql:42.2.21'
+    implementation 'org.postgresql:postgresql:42.2.22'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -217,7 +217,7 @@ dependencies {
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.7.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.7.2'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.11.2'
+    testImplementation 'net.bytebuddy:byte-buddy-parent:1.11.5'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
     testImplementation 'org.mockito:mockito-core:3.11.1'

diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -2,13 +2,17 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 import java.util.Locale;
 import java.util.Optional;
 import java.util.Set;
+import java.util.Vector;
 import java.util.prefs.BackingStoreException;
 
 import org.jabref.gui.Globals;
@@ -24,6 +28,7 @@
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.exporter.SavePreferences;
 import org.jabref.logic.exporter.TemplateExporter;
+import org.jabref.logic.exporter.XmpPdfExporter;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImportException;
 import org.jabref.logic.importer.ImportFormatReader;
@@ -49,6 +54,8 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.DummyFileUpdateMonitor;
+import org.jabref.model.util.FileHelper;
+import org.jabref.preferences.FilePreferences;
 import org.jabref.preferences.SearchPreferences;
 
 import com.google.common.base.Throwables;
@@ -215,6 +222,12 @@ private List<ParserResult> processArguments() {
             automaticallySetFileLinks(loaded);
         }
 
+        if (cli.isWriteXMPtoPdf()) {
+            if (!loaded.isEmpty()) {
+                writeXMPtoPdf(loaded, cli.getWriteXMPtoPdf(), Globals.prefs.getDefaultEncoding(), Globals.prefs.getXmpPreferences(), Globals.prefs.getFilePreferences());
+            }
+        }
+
         if (cli.isFileExport()) {
             if (!loaded.isEmpty()) {
                 exportFile(loaded, cli.getFileExport().split(","));
@@ -239,6 +252,88 @@ private List<ParserResult> processArguments() {
         return loaded;
     }
 
+    private void writeXMPtoPdf(List<ParserResult> loaded, String filesAndCitekeys, Charset encoding, XmpPreferences xmpPreferences, FilePreferences filePreferences) {
+        if (loaded.isEmpty()) {
+            LOGGER.error("The write xmp option depends on a valid import option.");
+            return;
+        }
+        ParserResult pr = loaded.get(loaded.size() - 1);
+        BibDatabaseContext databaseContext = pr.getDatabaseContext();
+        BibDatabase dataBase = pr.getDatabase();
+
+        XmpPdfExporter xmpPdfExporter = new XmpPdfExporter(xmpPreferences);
+
+        if ("all".equals(filesAndCitekeys)) {
+            for (BibEntry entry : dataBase.getEntries()) {
+                writeXMPtoPDFsOfEntry(databaseContext, entry.getCitationKey().orElse("<no cite key defined>"), entry, encoding, filePreferences, xmpPdfExporter);
+            }
+            return;
+        }
+
+        Vector<String> citeKeys = new Vector<>();
+        Vector<String> pdfs = new Vector<>();
+        for (String fileOrCiteKey : filesAndCitekeys.split(",")) {
+            if (fileOrCiteKey.toLowerCase(Locale.ROOT).endsWith(".pdf")) {
+                pdfs.add(fileOrCiteKey);
+            } else {
+                citeKeys.add(fileOrCiteKey);
+            }
+        }
+
+        writeXMPtoPdfByCitekey(databaseContext, dataBase, citeKeys, encoding, filePreferences, xmpPdfExporter);
+        writeXMPtoPdfByFileNames(databaseContext, dataBase, pdfs, encoding, filePreferences, xmpPdfExporter);
+
+    }
+
+    private void writeXMPtoPDFsOfEntry(BibDatabaseContext databaseContext, String citeKey, BibEntry entry, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter) {
+        try {
+            if (xmpPdfExporter.exportToAllFilesOfEntry(databaseContext, encoding, filePreferences, entry, Arrays.asList(entry))) {
+                LOGGER.info(String.format("Successfully written XMP metadata on at least one linked file of %s", citeKey));
+            } else {
+                LOGGER.error(String.format("Cannot write XMP metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.", citeKey));
+            }
+        } catch (Exception e) {
+            LOGGER.error(String.format("Failed writing XMP metadata on a linked file of %s.", citeKey));
+        }
+    }
+
+    private void writeXMPtoPdfByCitekey(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> citeKeys, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter) {
+        for (String citeKey : citeKeys) {
+            List<BibEntry> bibEntryList = dataBase.getEntriesByCitationKey(citeKey);
+            if (bibEntryList.isEmpty()) {
+                LOGGER.error(String.format("Skipped - Cannot find %s in library.", citeKey));
+                continue;
+            }
+            for (BibEntry entry : bibEntryList) {
+                writeXMPtoPDFsOfEntry(databaseContext, citeKey, entry, encoding, filePreferences, xmpPdfExporter);
+            }
+        }
+    }
+
+    private void writeXMPtoPdfByFileNames(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> fileNames, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter) {
+        for (String fileName : fileNames) {
+            Path filePath = Path.of(fileName);
+            if (!filePath.isAbsolute()) {
+                filePath = FileHelper.find(fileName, databaseContext.getFileDirectories(filePreferences)).orElse(FileHelper.find(fileName, Arrays.asList(Path.of("").toAbsolutePath())).orElse(filePath));
+            }
+            if (Files.exists(filePath)) {
+                try {
+                    if (xmpPdfExporter.exportToFileByPath(databaseContext, dataBase, encoding, filePreferences, filePath)) {
+                        LOGGER.info(String.format("Successfully written XMP metadata of at least one entry to %s", fileName));
+                    } else {
+                        LOGGER.error(String.format("File %s is not linked to any entry in database.", fileName));
+                    }
+                } catch (IOException e) {
+                    LOGGER.error("Error accessing files.", fileName);
+                } catch (Exception e) {
+                    LOGGER.error(String.format("Error writing entry to %s.", fileName));
+                }
+            } else {
+                LOGGER.error(String.format("Skipped - PDF %s does not exist", fileName));
+            }
+        }
+    }
+
     private boolean exportMatches(List<ParserResult> loaded) {
         String[] data = cli.getExportMatches().split(",");
         String searchTerm = data[0].replace("\\$", " "); // enables blanks within the search term:

diff --git a/src/main/java/org/jabref/cli/JabRefCLI.java b/src/main/java/org/jabref/cli/JabRefCLI.java
@@ -147,6 +147,14 @@ public boolean isAutomaticallySetFileLinks() {
         return cl.hasOption("automaticallySetFileLinks");
     }
 
+    public boolean isWriteXMPtoPdf() {
+        return cl.hasOption("writeXMPtoPdf");
+    }
+
+    public String getWriteXMPtoPdf() {
+        return cl.getOptionValue("writeXMPtoPdf");
+    }
+
     private static Options getOptions() {
         Options options = new Options();
 
@@ -242,6 +250,14 @@ private static Options getOptions() {
                 .argName("KEY1[,KEY2][,KEYn] | all")
                 .build());
 
+        options.addOption(Option
+                .builder("w")
+                .longOpt("writeXMPtoPdf")
+                .desc(String.format("%s: '%s'", Localization.lang("Write BibTeXEntry as XMP metadata to PDF."), "-w pathToMyOwnPaper.pdf"))
+                .hasArg()
+                .argName("CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all")
+                .build());
+
         return options;
     }
 

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
@@ -1236,3 +1236,7 @@ TextFlow * {
 .fontsizeSpinner{
     -fx-pref-width: 5em;
 }
+
+.text-field:invalid {
+    -fx-background-color: rgba(240, 128, 128, 0.5);
+}
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -4,7 +4,6 @@
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
@@ -1040,11 +1039,10 @@ public void addTab(LibraryTab libraryTab, boolean raisePanel) {
     }
 
     private void trackOpenNewDatabase(LibraryTab libraryTab) {
-        Map<String, String> properties = new HashMap<>();
-        Map<String, Double> measurements = new HashMap<>();
-        measurements.put("NumberOfEntries", (double) libraryTab.getBibDatabaseContext().getDatabase().getEntryCount());
-
-        Globals.getTelemetryClient().ifPresent(client -> client.trackEvent("OpenNewDatabase", properties, measurements));
+        Globals.getTelemetryClient().ifPresent(client -> client.trackEvent(
+                "OpenNewDatabase",
+                Map.of(),
+                Map.of("NumberOfEntries", (double) libraryTab.getBibDatabaseContext().getDatabase().getEntryCount())));
     }
 
     public LibraryTab addTab(BibDatabaseContext databaseContext, boolean raisePanel) {

diff --git a/src/main/java/org/jabref/gui/actions/JabRefAction.java b/src/main/java/org/jabref/gui/actions/JabRefAction.java
@@ -1,6 +1,5 @@
 package org.jabref.gui.actions;
 
-import java.util.HashMap;
 import java.util.Map;
 
 import javafx.beans.binding.Bindings;
@@ -77,10 +76,9 @@ private void trackExecute(String actionName) {
     }
 
     private void trackUserActionSource(String actionName, Sources source) {
-        Map<String, String> properties = new HashMap<>();
-        Map<String, Double> measurements = new HashMap<>();
-        properties.put("Source", source.toString());
-
-        Globals.getTelemetryClient().ifPresent(telemetryClient -> telemetryClient.trackEvent(actionName, properties, measurements));
+        Globals.getTelemetryClient().ifPresent(telemetryClient -> telemetryClient.trackEvent(
+                actionName,
+                Map.of("Source", source.toString()),
+                Map.of()));
     }
 }
diff --git a/src/main/java/org/jabref/gui/autocompleter/SuggestionProviders.java b/src/main/java/org/jabref/gui/autocompleter/SuggestionProviders.java
@@ -27,7 +27,6 @@ public SuggestionProviders() {
     }
 
     public SuggestionProvider<?> getForField(Field field) {
-
         if (isEmpty || !autoCompletePreferences.getCompleteFields().contains(field)) {
             return new EmptySuggestionProvider();
         }

diff --git a/src/main/java/org/jabref/gui/fieldeditors/JournalEditorViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/JournalEditorViewModel.java
@@ -22,8 +22,11 @@ public void toggleAbbreviation() {
             return;
         }
 
-        if (journalAbbreviationRepository.isKnownName(text.get())) {
-            Optional<String> nextAbbreviation = journalAbbreviationRepository.getNextAbbreviation(text.get());
+        // Ignore brackets when matching abbreviations.
+        final String name = StringUtil.ignoreCurlyBracket(text.get());
+
+        if (journalAbbreviationRepository.isKnownName(name)) {
+            Optional<String> nextAbbreviation = journalAbbreviationRepository.getNextAbbreviation(name);
 
             if (nextAbbreviation.isPresent()) {
                 text.set(nextAbbreviation.get());

diff --git a/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPane.java b/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPane.java
@@ -1,10 +1,12 @@
 package org.jabref.gui.importer.fetcher;
 
+import javafx.css.PseudoClass;
 import javafx.geometry.Pos;
 import javafx.scene.Node;
 import javafx.scene.control.Button;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.TextField;
+import javafx.scene.control.Tooltip;
 import javafx.scene.input.KeyCode;
 import javafx.scene.layout.HBox;
 import javafx.scene.layout.Priority;
@@ -31,6 +33,8 @@
 
 public class WebSearchPane extends SidePaneComponent {
 
+    private static final PseudoClass QUERY_INVALID = PseudoClass.getPseudoClass("invalid");
+
     private final PreferencesService preferences;
     private final WebSearchPaneViewModel viewModel;
 
@@ -75,6 +79,16 @@ protected Node createContentPane() {
         query.getStyleClass().add("searchBar");
 
         viewModel.queryProperty().bind(query.textProperty());
+        EasyBind.subscribe(viewModel.queryValidationStatus().validProperty(),
+                valid -> {
+                    if (!valid && viewModel.queryValidationStatus().getHighestMessage().isPresent()) {
+                        query.setTooltip(new Tooltip(viewModel.queryValidationStatus().getHighestMessage().get().getMessage()));
+                        query.pseudoClassStateChanged(QUERY_INVALID, true);
+                    } else {
+                        query.setTooltip(null);
+                        query.pseudoClassStateChanged(QUERY_INVALID, false);
+                    }
+                });
 
         // Allows to trigger search on pressing enter
         query.setOnKeyPressed(event -> {